Narsis Kiani

Publications
Grants
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Articles

Journal article: INFORMATION SCIENCES. 2025;720:122520
Minimal algorithmic information loss methods for dimension reduction, feature selection and network sparsification
Zenil H; Kiani NA; Adams A; Abrahao FS; Rueda-Toicen A; Zea AA; Ozelim L; Tegner J
Journal article: JOURNAL OF HEPATOLOGY. 2025;82:s54-s55
OS-077 Single-cell RNA sequencing of peripheral blood mononuclear cells in patients with acutely decompensated cirrhosis reveals a specific monocyte subset associated with an increased risk of progression to ACLF
Wirtz TH; Palomino S; Pollmanns MR; Huergo E; Schreibing F; Reißing J; Sanchez C; López-Vicario C; Aransay AM; Baldassarre M; Zaccherini G; Pompili E; Schulz M; Uschner FE; Klein S; Gu W; Schierwagen R; Valainathan S; Verbeeck A; Campion D; Giovo I; Koch A; Kramann R; Bruns T; Kiani N; Caraceni P; Alessandria C; Moreau R; Trebicka J; Clària J; Planell N; Rautou P-E; Trautwein C; Gómez-Cabrero D
Article: CARDIO-ONCOLOGY. 2025;11(1):5
Cardiovascular health in breast cancer patients: insight on BRCA1/2 mutations impact
Mallios P; Manshadi MD; Hubbert L; Aydin T; Maes C; Rantala J; Liljegren A; Kiani NA; Hedayati E
Article: PLOS COMPUTATIONAL BIOLOGY. 2024;20(12):e1012656
ClustAll: An R package for patient stratification in complex diseases
Ortega-Legarreta A; Palomino-Echeverria S; Huergo E; Lagani V; Kiani NA; Rautou P-E; Picola NP; Tegner J; Gomez-Cabrero D
Article: ISCIENCE. 2024;27(11):111122
A comparative analysis of blastoid models through single-cell transcriptomics
Balubaid A; Alsolami S; Kiani NA; Gomez-Cabrero D; Li M; Tegner J
Journal article: PLOS COMPLEX SYSTEMS. 2024;1(1):e0000014
Assembly Theory is an approximation to algorithmic complexity based on LZ compression that does not explain selection or evolution
Abrahão FS; Hernández-Orozco S; Kiani NA; Tegnér J; Zenil H
Article: JOURNAL OF TRANSLATIONAL MEDICINE. 2024;22(1):599
A robust clustering strategy for stratification unveils unique patient subgroups in acutely decompensated cirrhosis
Palomino-Echeverria S; Huergo E; Ortega-Legarreta A; Raposo EMU; Aguilar F; Pena-Ramirez CDL; Lopez-Vicario C; Alessandria C; Laleman W; Farias AQ; Moreau R; Fernandez J; Arroyo V; Caraceni P; Lagani V; Sanchez-Garrido C; Claria J; Tegner J; Trebicka J; Kiani NA; Planell N; Rautou P-E; Gomez-Cabrero D
Journal article: ESMO OPEN. 2024;9:103190
168P Cardiovascular risks in breast cancer: Insights from BRCA1/2 mutation carriers and sporadic cases
Mallios P; Hedayati E; Kiani N; Rantala J; Hubbert L; Liljegren A
Article: NATURE MACHINE INTELLIGENCE. 2023;5(12):1437-1446
Reusability report: Learning the transcriptional grammar in single-cell RNA-sequencing data using transformers
Khan SA; Maillo A; Lagani V; Lehmann R; Kiani NA; Gomez-Cabrero D; Tegner J
Journal article: QUANTITATIVE BIOLOGY. 2023;11(3):246-259
LIBRA: an adaptative integrative tool for paired single-cell multi-omics data
Martinez-de-Morentin X; Khan SA; Lehmann R; Qu S; Maillo A; Kiani NA; Prosper F; Tegner J; Gomez-Cabrero D
Article: BREAST. 2023;70:18-24
Risk-adjusted benchmarking of long-term overall survival in patients with HER2-positive early-stage Breast cancer: A Swedish retrospective cohort study
Thurell J; Manouchehri N; Fredriksson I; Wilking U; Bergh J; Ryden L; Koppert LB; Karsten MM; Kiani NA; Hedayati E
Journal article: JOURNAL OF HEPATOLOGY. 2023;78:s290
SAT-337 Robust identification of patient subgroups in acute decompensated cirrhosis
Palomino S; Huergo E; Uson E; Sanchez C; Lagani V; Kiani N; Planell N; Gurbindo U; Trebicka J; Farias AQ; Caraceni P; Rautou P-E; Gomez-Cabrero D
Article: CANCER MEDICINE. 2023;12(9):10840-10850
Planning for return to work during the first year after breast cancer metastasis: A Swedish cohort study
Johnsson A; Kiani NA; Gernaat SAM; Wilking U; Shabo I; Hedayati E
Article: PLOS ONE. 2023;18(2):e0281315
scAEGAN: Unification of single-cell genomics data by adversarial learning of latent space correspondences
Khan SA; Lehmann R; Martinez-de-Morentin X; Maillo A; Lagani V; Kiani NA; Gomez-Cabrero D; Tegner J
Article: PLOS COMPUTATIONAL BIOLOGY. 2023;19(2):e1010811
LSD-induced increase of Ising temperature and algorithmic complexity of brain dynamics
Ruffini G; Damiani G; Lozano-Soldevilla D; Deco N; Rosas FEE; Kiani NAA; Ponce-Alvarez A; Kringelbach MLL; Carhart-Harris R; Deco G
Article: EUROPEAN JOURNAL OF CANCER CARE. 2022;31(5):e13626
Use of sickness benefits by patients with metastatic breast cancer-A Swedish cohort study
Altena R; Gernaat SAM; Wilking U; Kiani NA; Johnsson A; Hedayati E
Article: NUCLEIC ACIDS RESEARCH. 2020;48(19):10867-10876
MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells
Sumida N; Sifakis EG; Kiani NA; Ronnegren AL; Scholz BA; Vestlund J; Gomez-Cabrero D; Tegner J; Gondor A; Ohlsson R
Journal article: DIAMOND AND RELATED MATERIALS. 2020;108:107987
Kinetic study on the copper electroless coating on carbon nanotubes
Shakibhamedan S; Kiani N; Sheibani S
Article: PLASMONICS. 2020;15(2):417-426
Polarization Controlling of Multi Resonant Graphene-Based Microstrip Antenna
Jafari Chashmi M; Rezaei P; Kiani N
Article: FRONTIERS IN ONCOLOGY. 2020;10:51
Immunometabolic Network Interactions of the Kynurenine Pathway in Cutaneous Malignant Melanoma
Rad Pour S; Morikawa H; Kiani NA; Gomez-Cabrero D; Hayes A; Zheng X; Pernemalm M; Lehtio J; Mole DJ; Hansson J; Eriksson H; Tegner J
Article: FRONTIERS IN ARTIFICIAL INTELLIGENCE. 2020;3:567356
Algorithmic Probability-Guided Machine Learning on Non-Differentiable Spaces
Hernandez-Orozco S; Zenil H; Riedel J; Uccello A; Kiani NA; Tegner J
Article: OPTIK. 2020;200:163321
Y-shaped graphene-based antenna with switchable circular polarization
Chashmi MJ; Rezaei P; Kiani N
Article: ISCIENCE. 2019;19:1160-1172
An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems
Zenil H; Kiani NA; Marabita F; Deng Y; Elias S; Schmidt A; Ball G; Tegner J
Article: SCIENTIFIC REPORTS. 2019;9(1):12150
Exhaustion of CD4+T-cells mediated by the Kynurenine Pathway in Melanoma
Pour SR; Morikawa H; Kiani N; Yang M; Azimi A; Shafi G; Shang M; Baumgartner R; Ketelhuth DFJ; Kamleh MA; Wheelock CE; Lundqvist A; Hansson J; Tegner J
Article: JOURNAL OF LEUKOCYTE BIOLOGY. 2019;106(2):413-430
Phosphatase inhibitor PPP1R11 modulates resistance of human T cells toward Treg-mediated suppression of cytokine expression
Joshi RN; Fernandes SJ; Shang M-M; Kiani NA; Gomez-Cabrero D; Tegner J; Schmidt A
Article: NATURE COMMUNICATIONS. 2019;10(1):2674
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
Menden MP; Wang D; Mason MJ; Szalai B; Bulusu KC; Guan Y; Yu T; Kang J; Jeon M; Wolfinger R; Nguyen T; Zaslavskiy M; Jang IS; Ghazoui Z; Ahsen ME; Vogel R; Neto EC; Norman T; Tang EKY; Garnett MJ; Di Veroli GY; Fawell S; Stolovitzky G; Guinney J; Dry JR; Saez-Rodriguez J; Abante J; Abecassis BS; Aben N; Aghamirzaie D; Aittokallio T; Akhtari FS; Al-lazikani B; Alam T; Allam A; Allen C; de Almeida MP; Altarawy D; Alves V; Amadoz A; Anchang B; Antolin AA; Ash JR; Romeo Aznar V; Ba-alawi W; Bagheri M; Bajic V; Ball G; Ballester PJ; Baptista D; Bare C; Bateson M; Bender A; Bertrand D; Wijayawardena B; Boroevich KA; Bosdriesz E; Bougouffa S; Bounova G; Brouwer T; Bryant B; Calaza M; Calderone A; Calza S; Capuzzi S; Carbonell-Caballero J; Carlin D; Carter H; Castagnoli L; Celebi R; Cesareni G; Chang H; Chen G; Chen H; Chen H; Cheng L; Chernomoretz A; Chicco D; Cho K-H; Cho S; Choi D; Choi J; Choi K; Choi M; De Cock M; Coker E; Cortes-Ciriano I; Cserzo M; Cubuk C; Curtis C; Van Daele D; Dang CC; Dijkstra T; Dopazo J; Draghici S; Drosou A; Dumontier M; Ehrhart F; Eid F-E; ElHefnawi M; Elmarakeby H; van Engelen B; Engin HB; de Esch I; Evelo C; Falcao AO; Farag S; Fernandez-Lozano C; Fisch K; Flobak A; Fornari C; Foroushani ABK; Fotso DC; Fourches D; Friend S; Frigessi A; Gao F; Gao X; Gerold JM; Gestraud P; Ghosh S; Gillberg J; Godoy-Lorite A; Godynyuk L; Godzik A; Goldenberg A; Gomez-Cabrero D; Gonen M; de Graaf C; Gray H; Grechkin M; Guimera R; Guney E; Haibe-Kains B; Han Y; Hase T; He D; He L; Heath LS; Hellton KH; Helmer-Citterich M; Hidalgo MR; Hidru D; Hill SM; Hochreiter S; Hong S; Hovig E; Hsueh Y-C; Hu Z; Huang JK; Huang RS; Hunyady L; Hwang J; Hwang TH; Hwang W; Hwang Y; Isayev O; Walk OBD; Jack J; Jahandideh S; Ji J; Jo Y; Kamola PJ; Kanev GK; Karacosta L; Karimi M; Kaski S; Kazanov M; Khamis AM; Khan SA; Kiani NA; Kim A; Kim J; Kim J; Kim K; Kim K; Kim S; Kim Y; Kim Y; Kirk PDW; Kitano H; Klambauer G; Knowles D; Ko M; Kohn-Luque A; Kooistra AJ; Kuenemann MA; Kuiper M; Kurz C; Kwon M; van Laarhoven T; Laegreid A; Lederer S; Lee H; Lee J; Lee YW; Leppaho E; Lewis R; Li J; Li L; Liley J; Lim WK; Lin C; Liu Y; Lopez Y; Low J; Lysenko A; Machado D; Madhukar N; De Maeyer D; Malpartida AB; Mamitsuka H; Marabita F; Marchal K; Marttinen P; Mason D; Mazaheri A; Mehmood A; Mehreen A; Michaut M; Miller RA; Mitsopoulos C; Modos D; Van Moerbeke M; Moo K; Motsinger-Reif A; Movva R; Muraru S; Muratov E; Mushthofa M; Nagarajan N; Nakken S; Nath A; Neuvial P; Newton R; Ning Z; De Niz C; Oliva B; Olsen C; Palmeri A; Panesar B; Papadopoulos S; Park J; Park S; Park S; Pawitan Y; Peluso D; Pendyala S; Peng J; Perfetto L; Pirro S; Plevritis S; Politi R; Poon H; Porta E; Prellner I; Preuer K; Angel Pujana M; Ramnarine R; Reid JE; Reyal F; Richardson S; Ricketts C; Rieswijk L; Rocha M; Rodriguez-Gonzalvez C; Roell K; Rotroff D; de Ruiter JR; Rukawa P; Sadacca B; Safikhani Z; Safitri F; Sales-Pardo M; Sauer S; Schlichting M; Seoane JA; Serra J; Shang M-M; Sharma A; Sharma H; Shen Y; Shiga M; Shin M; Shkedy Z; Shopsowitz K; Sinai S; Skola D; Smirnov P; Soerensen IF; Soerensen P; Song J-H; Song SO; Soufan O; Spitzmueller A; Steipe B; Suphavilai C; Tamayo SP; Tamborero D; Tang J; Tanoli Z-U; Tarres-Deulofeu M; Tegner J; Thommesen L; Tonekaboni SAM; Tran H; De Troyer E; Truong A; Tsunoda T; Turu G; Tzeng G-Y; Verbeke L; Videla S; Vis D; Voronkov A; Votis K; Wang A; Wang H-QH; Wang P-W; Wang S; Wang W; Wang X; Wang X; Wennerberg K; Wernisch L; Wessels L; van Westen GJP; Westerman BA; White SR; Willighagen E; Wurdinger T; Xie L; Xie S; Xu H; Yadav B; Yau C; Yeerna H; Yin JW; Yu M; Yu M; Yun SJ; Zakharov A; Zamichos A; Zanin M; Zeng L; Zenil H; Zhang F; Zhang P; Zhang W; Zhao H; Zhao L; Zheng W; Zoufir A; Zucknick M
Article: ENTROPY. 2019;21(6):E560-560
The Thermodynamics of Network Coding, and an Algorithmic Refinement of the Principle of Maximum Entropy
Zenil H; Kiani NA; Tegner J
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2019;116(19):9671-9676
MAPK pathway and B cells overactivation in multiple sclerosis revealed by phosphoproteomics and genomic analysis
Kotelnikova E; Kiani NA; Messinis D; Pertsovskaya I; Pliaka V; Bernardo-Faura M; Rinas M; Vila G; Zubizarreta I; Pulido-Valdeolivas I; Sakellaropoulos T; Faigle W; Silberberg G; Masso M; Stridh P; Behrens J; Olsson T; Martin R; Paul F; Alexopoulos LG; Saez-Rodriguez J; Tegner J; Villoslada P
Article: OPTIK. 2019;184:421-427
Reconfigurable graphene-based V-shaped dipole antenna: From quasi-isotropic to directional radiation pattern
Chashmi MJ; Rezaei P; Kiani N
Article: NATURE MACHINE INTELLIGENCE. 2019;1(1):58-66
Causal deconvolution by algorithmic generative models
Zenil H; Kiani NA; Zea AA; Tegner J
Article: ENTROPY. 2018;20(8):E605-605
A Decomposition Method for Global Evaluation of Shannon Entropy and Local Estimations of Algorithmic Complexity
Zenil H; Hernandez-Orozco S; Kiani NA; Soler-Toscano F; Rueda-Toicen A; Tegner J
Article: ROYAL SOCIETY OPEN SCIENCE. 2018;5(8):180399
Algorithmically probable mutations reproduce aspects of evolution, such as convergence rate, genetic memory and modularity
Hernandez-Orozco S; Kiani NA; Zenil H
Article: ENTROPY. 2018;20(7):E534-534
Symmetry and Correspondence of Algorithmic Complexity over Geometric, Spatial and Topological Representations
Zenil H; Kiani NA; Tegner J
Article: BMC BIOLOGY. 2018;16(1):47
Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3
Schmidt A; Marabita F; Kiani NA; Gross CC; Johansson HJ; Elias S; Rautio S; Eriksson M; Fernandes SJ; Silberberg G; Ullah U; Bhatia U; Lahdesmaki H; Lehtio J; Gomez-Cabrero D; Wiendl H; Lahesmaa R; Tegner J
Journal article: PARALLEL PROCESSING LETTERS. 2018;28(1):1850005
Algorithmic Complexity and Reprogrammability of Chemical Structure Networks
Zenil H; Kiani NA; Shang M-M; Tegner J
Article: JOURNAL OF TRANSLATIONAL MEDICINE. 2018;16(1):34
Network modules uncover mechanisms of skeletal muscle dysfunction in COPD patients
Tenyi A; Cano I; Marabita F; Kiani N; Kalko SG; Barreiro E; de Atauri P; Cascante M; Gomez-Cabrero D; Roca J
Article: BIOINFORMATICS. 2017;33(24):3964-3972
HiDi: an efficient reverse engineering schema for large-scale dynamic regulatory network reconstruction using adaptive differentiation
Deng Y; Zenil H; Tegner J; Kiani NA
Article: PLOS COMPUTATIONAL BIOLOGY. 2017;13(10):e1005757
Dynamics and heterogeneity of brain damage in multiple sclerosis
Kotelnikova E; Kiani NA; Abad E; Martinez-Lapiscina EH; Andorra M; Zubizarreta I; Pulido-Valdeolivas I; Pertsovskaya I; Alexopoulos LG; Olsson T; Martin R; Paul F; Tegner J; Garcia-Ojalvo J; Villoslada P
Article: PHYSICAL REVIEW E. 2017;96(1):012308
Low-algorithmic-complexity entropy-deceiving graphs
Zenil H; Kiani NA; Tegner J
Article: MATHEMATICAL BIOSCIENCES. 2017;289:1-8
A minimal unified model of disease trajectories captures hallmarks of multiple sclerosis
Kannan V; Kiani NA; Piehl F; Tegner J
Journal article: JOURNAL OF COMPLEX NETWORKS. 2016;4(3):342-362
Quantifying loss of information in network-based dimensionality reduction techniques
Zenil H; Kiani NA; Tegner J
Article: SCIENTIFIC REPORTS. 2016;6:26170
Conditional Disease Development extracted from Longitudinal Health Care Cohort Data using Layered Network Construction
Kannan V; Swartz F; Kiani NA; Silberberg G; Tsipras G; Gomez-Cabrero D; Alexanderson K; Tegner J
Article: MULTIPLE SCLEROSIS JOURNAL. 2015;21(2):138-146
Signaling networks in MS: A systems-based approach to developing new pharmacological therapies
Kotelnikova E; Bernardo-Faura M; Silberberg G; Kiani NA; Messinis D; Melas IN; Artigas L; Schwartz E; Mazo I; Masso M; Alexopoulos LG; Manuel Mas J; Olsson T; Tegner J; Martin R; Zamora A; Paul F; Saez-Rodriguez J; Villoslada P
Article: SOFT COMPUTING. 2014;18(12):2461-2469
Laplace transform formula on fuzzy nth-order derivative and its application in fuzzy ordinary differential equations
Ahmadi MB; Kiani NA; Mikaeilvand N
Article: JOURNAL OF TRANSLATIONAL MEDICINE. 2014;12(Suppl 2):S4
Systems Medicine: from molecular features and models to the clinic in COPD
Gomez-Cabrero D; Menche J; Cano I; Abugessaisa I; Huertas-Miguelanez M; Tenyi A; Marin de Mas I; Kiani NA; Marabita F; Falciani F; Burrowes K; Maier D; Wagner P; Selivanov V; Cascante M; Roca J; Barabasi A-L; Tegner J
Article: BMC BIOINFORMATICS. 2014;15(1):250
Dynamic probabilistic threshold networks to infer signaling pathways from time-course perturbation data
Kiani NA; Kaderali L
Article: ANNALS OF OPERATIONS RESEARCH. 2012;196(1):459-468
Resource allocation for performance improvement
Nasrabadi N; Dehnokhalaji A; Kiani NA; Korhonen PJ; Wallenius J
Article: BMC BIOINFORMATICS. 2011;12:485
Normalizing for individual cell population context in the analysis of high-content cellular screens
Knapp B; Rebhan I; Kumar A; Matula P; Kiani NA; Binder M; Erfle H; Rohr K; Eils R; Bartenschlager R; Kaderali L
Article: INTERNATIONAL JOURNAL OF UNCERTAINTY FUZZINESS AND KNOWLEDGE-BASED SYSTEMS. 2011;19(6):999-1012
DEGENERACY IN FUZZY LINEAR PROGRAMMING AND ITS APPLICATION
Sigarpich LA; Allahviranloo T; Lotfi FH; Kiani NA
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 2011;286(31):27278-27287
Molecular Mechanism of Signal Perception and Integration by the Innate Immune Sensor Retinoic Acid-inducible Gene-I (RIG-I)
Binder M; Eberle F; Seitz S; Muecke N; Hueber CM; Kiani N; Kaderali L; Lohmann V; Dalpke A; Bartenschlager R
Article: INFORMATION SCIENCES. 2009;179(8):1207-1215
Toward the existence and uniqueness of solutions of second-order fuzzy differential equations
Allahviranloo T; Kiani NA; Barkhordari M
Article: INFORMATION SCIENCES. 2009;179(7):956-966
Solving fuzzy differential equations by differential transformation method
Allahviranloo T; Kiani NA; Motamedi N
Journal article: APPLICATIONS AND APPLIED MATHEMATICS-AN INTERNATIONAL JOURNAL. 2008;3(1):77-88
Signed Decomposition of Fully Fuzzy Linear Systems
Allahviranloo T; Mikaeilvand N; Kiani NA; Shabestari RM
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All other publications

Preprint: MEDRXIV. 2025
Single-cell profiling reveals monocyte mitochondrial dysfunction in patients with cirrhosis progressing to acute-on-chronic liver failure
Wirtz TH; Palomino-Echeverria S; Pollmanns MR; Huergo E; Schreibing F; Reißing J; Sánchez-Garrido C; López-Vicario C; Aransay AM; Baldassare M; Zaccherini G; Pompili E; Schulz M; Uschner FE; Klein S; Gu W; Schierwagen R; Valainathan S; Verbeeck A; Campion D; Giovo I; Schneider KM; Koch A; Kramann R; Bruns T; Kiani N; Stiles L; Caraceni P; Alessandria C; Moreau R; Trebicka J; Clària J; Planell N; Rautou P-E; Trautwein C; Gomez-Cabrero D
Preprint: ARXIV. 2024
Assembly Theory Reduced to Shannon Entropy and Rendered Redundant by Naive Statistical Algorithms
Ozelim L; Uthamacumaran A; Abrahão FS; Hernández-Orozco S; Kiani NA; Tegnér J; Zenil H
Review: NPJ SYSTEMS BIOLOGY AND APPLICATIONS. 2024;10(1):82
On the salient limitations of the methods of assembly theory and their classification of molecular biosignatures
Uthamacumaran A; Abrahao FS; Kiani NA; Zenil H
Preprint: BIORXIV. 2024
PrePR-CT: Predicting Perturbation Responses in Unseen Cell Types Using Cell-Type-Specific Graphs
Alsulami R; Lehmann R; Khan SA; Lagani V; Gómez-Cabrero D; Kiani NA; Tegner J
Preprint: ARXIV. 2024
T- Hop: A framework for studying the importance path information in molecular graphs for chemical property prediction
Ibraheem A; Kiani N; Tegner J
Preprint: BIORXIV. 2024
SpatialDiffusion: Predicting Spatial Transcriptomics with Denoising Diffusion Probabilistic Models
Khan SA; Lagani V; Lehmann R; Kiani N; Gomez-Cabrero D; Tegner J
Preprint: ARXIV. 2024
Assembly Theory is an approximation to algorithmic complexity based on LZ compression that does not explain selection or evolution
Abrahão FS; Hernández-Orozco S; Kiani NA; Tegnér J; Zenil H
Preprint: BIORXIV. 2023
Joint Learning of Node Semantics and Graph Topology using a Transformer in the sparse network regime
Ubingazhibov A; Gomez-Cabrero D; Kiani NA; Tegner J
Preprint: MEDRXIV. 2023
ClustALL: A robust clustering strategy for stratification of patients with acutely decompensated cirrhosis
Palomino-Echeverria S; Huergou E; Ortega-Legarre A; Uson EM; Aguilar F; de la Pena C; Lopez-Vicario C; Alessandria C; Laleman W; Queiroz AF; Moreau R; Fernandez J; Arroyo V; Caraceni P; Lagani V; Sanchez C; Claria J; Tegner J; Trebicka J; Kiani N; Planell N; Rautou P-E; Gomez-Cabrero D
Meeting abstract: BLOOD. 2023;142:4044
Uncovering the Cis-Regulatory Program of Early Human B-Cell Commitment and Its Implications in the Pathogenesis of B-Cell Acute Lymphoblastic Leukemia
Planell N; Martinez-de-Morentin X; Mouzo D; Lara-Astiaso D; Vilas-Zornoza A; San-Martin P; Alignani D; Paiva B; Maillo A; Kurowska A; Urdangarin A; Noori P; Ortega-Legarreta A; Hernaez M; Lagani V; Kiani N; Subero IIM; Ramirez RN; Tegner J; Prosper F; Gomez-Cabrero D
Preprint: BIORXIV. 2023
Foundation Models Meet Imbalanced Single-Cell Data When Learning Cell Type Annotations
Alsabbagh AR; de Infante AMR; Gomez-Cabrero D; Kiani N; Khan SA; Tegnér J
Preprint: ARXIV. 2023
Whispering LLaMA: A Cross-Modal Generative Error Correction Framework for Speech Recognition
Radhakrishnan S; Yang C-HH; Khan SA; Kumar R; Kiani NA; Gomez-Cabrero D; Tegner JN
Conference publication: MULTIPLE SCLEROSIS JOURNAL. 2023;29:479-480
Exploring genetic clustering of severity markers to identify groups with reduced heterogeneity in multiple sclerosis
Stridh P; Shchetynsky K; Harroud A; Moridi T; Moylett S; Pukaj A; Esposito F; Gasperi C; Kiani N; Harbo HF; Saarela J; Giovanni MBF; Alfredsson L; Hillert J; Olsson T; Goris A; Hemmer B; Jagodic M; Cotsapas C; Kockum I
Conference publication: 2023;:1958-1962
A Parameter-Efficient Learning Approach to Arabic Dialect Identification with Pre-Trained General-Purpose Speech Model
Radhakrishnan S; Yang C-HH; Khan SA; Kiani NA; Gomez-Cabrero D; Tegner JN
Preprint: BIORXIV. 2023
Uncovering the regulatory landscape of early human B-cell lymphopoiesis and its implications in the pathogenesis of B-cell acute lymphoblastic leukemia
Planell N; Martínez-de-Morentin X; Mouzo D; Lara-Astiaso D; Vilas-Zornoza A; San Martín-Uriz P; Alignani D; Paiva B; Maillo A; Kurowska A; Berastegui N; Garcia-Olloqui P; Urdangarin A; Noori P; Ortega-Legarreta A; Hernaez M; Lagani V; Kiani N; Merkenschlager M; Ezponda T; Martín-Subero JI; Ramírez RN; Tegner J; Prosper F; Gomez-Cabrero D
Book: 2023
Algorithmic Information Dynamics
Zenil H; Kiani NA; Tegnér J
Preprint: ARXIV. 2023
A Parameter-Efficient Learning Approach to Arabic Dialect Identification with Pre-Trained General-Purpose Speech Model
Radhakrishnan S; Yang C-HH; Khan SA; Kiani NA; Gomez-Cabrero D; Tegner JN
Preprint: ARXIV. 2023
IHCV: Discovery of Hidden Time-Dependent Control Variables in Non-Linear Dynamical Systems
Munoz J; Balsamy S; Bernal-Tamayo JP; Balubaid A; de Infante AMR; Lagani V; Gomez-Cabrero D; Kiani NA; Tegner J
Preprint: BIORXIV. 2023
LEP-AD: Language Embedding of Proteins and Attention to Drugs predicts drug target interactions
Daga A; Khan SA; Cabrero DG; Hoehndorf R; Kiani N; Tegner J
Conference publication: 2023;:10007-10016
Whispering LLaMA: A Cross-Modal Generative Error Correction Framework for Speech Recognition
Radhakrishnan S; Yang C-H; Khan S; Kumar R; Kiani N; Gomez-Cabrero D; Tegnér J
Conference publication: MULTIPLE SCLEROSIS JOURNAL. 2022;28(3_SUPPL):172-173
A susceptibility network analysis of disease pathways leading to multiple sclerosis
Manouchehrinia A; Ebrahimi A; Wiil UK; Kiani NA; Lio P; Olsson T; Kockum I
Preprint: ARXIV. 2022
On the Salient Limitations of the Methods of Assembly Theory and their Classification of Molecular Biosignatures
Uthamacumaran A; Abrahão FS; Kiani NA; Zenil H
Preprint: BIORXIV. 2022
LSD-induced increase of Ising temperature and algorithmic complexity of brain dynamics
Ruffini G; Damiani G; Lozano-Soldevilla D; Deco N; Rosas F; Kiani N; Ponce-Alvarez A; Kringelbach M; Carhart-Harris R; Deco G
Preprint: BIORXIV. 2022
scAEGAN: Unification of Single-Cell Genomics Data by Adversarial Learning of Latent Space Correspondences
Khan SA; Lehmann R; Martinez-de-Morentin X; Ruiz AM; Lagani V; Kiani N; Gomez-Cabrero D; Tegner J
Book chapter: AUTOMATA AND COMPLEXITY: EMERGENCE, COMPLEXITY AND COMPUTATION. 2022;p. 433-453
Model Discovery and Discrete Inverse Problems with Cellular Automata and Boolean Networks
Zenil H; Zhang Y; Kiani NA
Book chapter: WSPC BOOK SERIES IN UNCONVENTIONAL COMPUTING. 2021;p. 171-219
Estimations of Integrated Information Based on Algorithmic Complexity and Dynamic Querying
Hernández-Espinosa A; Zenil H; Kiani NA; Tegnér J
Preprint: RESEARCH SQUARE. 2021
Use of Sickness Benefits by Patients With Metastatic Breast Cancer – A Swedish Cohort Study
Altena R; Gernaat SAM; Wilking U; Kiani N; Johnsson A; Hedayati E
Review: CARDIO-ONCOLOGY. 2021;7(1):20
Evidence-based prediction and prevention of cardiovascular morbidity in adults treated for cancer
Altena R; Hubbert L; Kiani NA; Wengstrom Y; Bergh J; Hedayati E
Preprint: BIORXIV. 2021
Adaptative Machine Translation between paired Single-Cell Multi-Omics Data
Martinez-de-Morentin X; Khan S; Lehmann R; Qu S; Maillo A; Kiani N; Prosper F; Tegner J; Gomez-Cabrero D
Preprint: BIORXIV. 2020
scMomentum: Inference of Cell-Type-Specific Regulatory Networks and Energy Landscapes
Soto L; Bernal-Tamayo J; Lehmann R; Balsamy S; Martinez-de-Morentin X; Vilas-Zornoza A; San-Martin P; Prosper F; Gomez-Cabrero D; Kiani N; Tegner J
Preprint: ARXIV. 2020
Evolving Neural Networks through a Reverse Encoding Tree
Zhang H; Yang C-HH; Zenil H; Kiani NA; Shen Y; Tegner JN
Preprint: ARXIV. 2019
Algorithmic Probability-guided Supervised Machine Learning on Non-differentiable Spaces
Hernández-Orozco S; Zenil H; Riedel J; Uccello A; Kiani NA; Tegnér J
Preprint: ARXIV. 2019
Estimations of Integrated Information Based on Algorithmic Complexity and Dynamic Querying
Hernández-Espinosa A; Zenil H; Kiani NA; Tegnér J
Book chapter: FROM PARALLEL TO EMERGENT COMPUTING. 2019;p. 367-384
Algorithmic Information Dynamics of Emergent, Persistent, and Colliding Particles in the Game of Life *
Zenil H; Kiani NA; Tegnér J
Preprint: ARXIV. 2018
Controllability, Multiplexing, and Transfer Learning in Networks using Evolutionary Learning
Ooi R; Yang C-HH; Chen P-Y; Eguìluz V; Kiani N; Zenil H; Gomez-Cabrero D; Tegnèr J
Review: ENTROPY. 2018;20(8):E551-551
A Review of Graph and Network Complexity from an Algorithmic Information Perspective
Zenil H; Kiani NA; Tegner J
Preprint: ARXIV. 2018
The Thermodynamics of Network Coding, and an Algorithmic Refinement of the Principle of Maximum Entropy
Zenil H; Kiani NA; Tegnér J
Preprint: BIORXIV. 2018
The ultra-sensitive Nodewalk technique identifies stochastic from virtual, population-based enhancer hubs regulatingMYCin 3D: Implications for the fitness of cancer cells
Sumida N; Sifakis E; Scholz B; Fernandez-Woodbridge A; Kiani N; Gomez-Cabrero D; Svensson P; Tegner J; Göndör A; Ohlsson R
Preprint: ARXIV. 2018
Symmetry and Algorithmic Complexity of Polyominoes and Polyhedral Graphs
Zenil H; Kiani NA; Tegnér J
Preprint: ARXIV. 2018
Algorithmic Causal Deconvolution of Intertwined Programs and Networks by Generative Mechanism
Zenil H; Kiani NA; Zea AA; Tegnér J
Preprint: ARXIV. 2018
Algorithmic Information Dynamics of Persistent Patterns and Colliding Particles in the Game of Life
Zenil H; Kiani NA; Tegnér J
Preprint: ARXIV. 2018
Algorithmic Complexity and Reprogrammability of Chemical Structure Networks
Zenil H; Kiani NA; Shang M-M; Tegnér J
Preprint: ARXIV. 2018
Minimal Algorithmic Information Loss Methods for Dimension Reduction, Feature Selection and Network Sparsification
Zenil H; Kiani NA; Adams A; Abrahão FS; Rueda-Toicen A; Zea AA; Ozelim L; Tegnér J
Preprint: ARXIV. 2018
Predictive Systems Toxicology
Kiani NA; Shang M-M; Zenil H; Tegnér J
Preprint: SSRN ELECTRONIC JOURNAL. 2018
An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems
Zenil H; Kiani NA; Marabita F; Deng Y; Elias S; Schmidt A; Ball G; Tegnér J
Review: METHODS IN MOLECULAR BIOLOGY. 2018;1800:535-557
Predictive Systems Toxicology.
Kiani NA; Shang M-M; Zenil H; Tegner J
Preprint: ARXIV. 2017
An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems
Zenil H; Kiani NA; Marabita F; Deng Y; Elias S; Schmidt A; Ball G; Tegnér J
Preprint: BIORXIV. 2017
An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems
Zenil H; Kiani N; Marabita F; Deng Y; Elias S; Schmidt A; Ball G; Tegnér J
Preprint: ARXIV. 2017
Algorithmically probable mutations reproduce aspects of evolution such as convergence rate, genetic memory, and modularity
Hernández-Orozco S; Kiani NA; Zenil H
Preprint: ARXIV. 2017
HiDi: An efficient reverse engineering schema for large scale dynamic regulatory network reconstruction using adaptive differentiation
Deng Y; Zenil H; Tégner J; Kiani NA
Corrigendum: SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY. 2016;60:168
Methods of information theory and algorithmic complexity for network biology (vol 51, pg 32, 2016)
Zenil H; Kiani NA; Tegner J
Review: PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES. 2016;374(2080):20160144
A perspective on bridging scales and design of models using low-dimensional manifolds and data-driven model inference
Tegner J; Zenil H; Kiani NA; Ball G; Gomez-Cabrero D
Preprint: ARXIV. 2016
A Decomposition Method for Global Evaluation of Shannon Entropy and Local Estimations of Algorithmic Complexity
Zenil H; Hernández-Orozco S; Kiani NA; Soler-Toscano F; Rueda-Toicen A
Preprint: ARXIV. 2016
Low Algorithmic Complexity Entropy-deceiving Graphs
Zenil H; Kiani N; Tegnér J
Review: SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY. 2016;51:44-52
Evaluating network inference methods in terms of their ability to preserve the topology and complexity of genetic networks
Kiani NA; Zenil H; Olczak J; Tegner J
Review: SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY. 2016;51:32-43
Methods of information theory and algorithmic complexity for network biology
Zenil H; Kiani NA; Tegner J
Review: CURRENT PHARMACEUTICAL DESIGN. 2016;22(46):6911-6917
Systems Toxicology: Systematic Approach to Predict Toxicity
Kiani NA; Shang M-M; Tegner J
Preprint: ARXIV. 2015
Evaluating Network Inference Methods in Terms of Their Ability to Preserve the Topology and Complexity of Genetic Networks
Kiani NA; Zenil H; Olczak J; Tegnér J
Conference publication: 2015 11TH INTERNATIONAL CONFERENCE ON SIGNAL-IMAGE TECHNOLOGY & INTERNET-BASED SYSTEMS (SITIS). 2015;:468-473
Topological Evaluation of Methods for Reconstruction of Genetic Regulatory Networks
Olczak J; Kiani NA; Zenil H; Tegner J
Preprint: ARXIV. 2015
Quantifying Loss of Information in Network-based Dimensionality Reduction Techniques
Zenil H; Kiani NA; Tegnér J
Preprint: ARXIV. 2015
Numerical Investigation of Graph Spectra and Information Interpretability of Eigenvalues
Zenil H; Kiani NA; Tegnér J
Book chapter: LECTURE NOTES IN COMPUTER SCIENCE. 2015;p. 395-405
Numerical Investigation of Graph Spectra and Information Interpretability of Eigenvalues
Zenil H; Kiani NA; Tegner J
Preprint: ARXIV. 2014
Methods of Information Theory and Algorithmic Complexity for Network Biology
Zenil H; Kiani NA; Tegnér J
Conference publication: 2013 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM). 2013;:74-76
Algorithmic complexity of motifs clusters superfamilies of networks
Zenil H; Kiani NA; Tegner J
Review: WORLD J VIROL. 2013;2(2):18-31
High-throughput RNA interference screens integrative analysis: Towards a comprehensive understanding of the virus-host interplay.
Amberkar S; Kiani NA; Bartenschlager R; Alvisi G; Kaderali L
Book chapter: ENCYCLOPEDIA OF SYSTEMS BIOLOGY. 2013;p. 2108-2110
Systems Virology
Kiani NA; Kaderali L
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Improving prediction and prognosis of multiple sclerosis; algorithmic approaches and biomarkers
Swedish Research Council
1 January 2025 - 31 December 2028
Fighting Multiple Sclerosis with Mathematics
VINNOVA
1 January 2014 - 1 May 2017

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